From 9d961cf84e3634976c28e85fdea8850290e4661b Mon Sep 17 00:00:00 2001
From: nilsberglund-orleans
 <83530463+nilsberglund-orleans@users.noreply.github.com>
Date: Tue, 28 Dec 2021 15:52:05 +0100
Subject: [PATCH] Update README.md

---
 README.md | 22 ++++++++++++++++++++--
 1 file changed, 20 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 5277354..0842fd0 100644
--- a/README.md
+++ b/README.md
@@ -6,7 +6,7 @@ C code for videos on YouTube Channel https://www.youtube.com/c/NilsBerglund
 
 Parameter values used in specific simulations will be gradually added to file `Parameters.md`, `Parameters_June21.md` and so on.
 
-There are two groups of 5 files and 11 files. 
+There are three groups of 5 files, 11 files and 3 files. 
 In addition the following files handling color schemes have been included:
 
 1. `hsluv.c`and `hsluv.h` from https://github.com/adammaj1/hsluv-color-gradient 
@@ -50,7 +50,7 @@ in the shell before running the program
 7. *wave_comparison.c*: comparison of the wave equation in two different domains
 8. *wave_energy.c*:     a version of `wave_billiard` plotting the energy profile of the wave
 9. *mangrove.c*:        a version of `wave_billiard` with additional features to animate mangroves
-10. *heat.c*:            simulation of the heat equation, with optional drawing of gradient field lines
+10. *heat.c*:           simulation of the heat equation, with optional drawing of gradient field lines
 11. *schrodinger.c*:    simulation of the Schrodinger equation
 
 - Create subfolders `tif_wave`, `tif_heat`, `tif_schrod`
@@ -75,10 +75,28 @@ in the shell before running the program
 
 `ffmpeg -i wave.%05d.tif -vcodec libx264 wave.mp4`
 
+### Molecular dynamics simulations
+
+1. *global_ljones.c*:     global variables and parameters
+2. *sub_lj.c*:            some drawing and initialization routines
+3. *lennardjones.c*:      simulation of molecular dynamics
+
+- Create subfolders `tif_ljones`
+- Customize constants at beginning of .c file
+- Compile with 
+
+`gcc -o lennardjones lennardjones.c -L/usr/X11R6/lib -ltiff -lm -lGL -lGLU -lX11 -lXmu -lglut -O3 -fopenmp`
+
+- Generate movie with 
+
+`ffmpeg -i lennardjones.%05d.tif -vcodec libx264 lennardjones.mp4`
+
 #### Some references ####
 
 - Discretizing the wave equation: https://hplgit.github.io/fdm-book/doc/pub/wave/pdf/wave-4print.pdf
 - Absorbing boundary conditions: https://hal.archives-ouvertes.fr/hal-01374183
 - Cloaking device: https://www.sciencedirect.com/science/article/pii/S0165212514001759
 - Poisson disc sampling: https://bl.ocks.org/mbostock/dbb02448b0f93e4c82c3
+- Thermostat algorithm: https://doi.org/10.1007/s10955-009-9734-0
+http://www.maths.warwick.ac.uk/~theil/HL12-3-2009.pdf